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What image file types will this plugin automatically add Shadowbox to?

bmp, gif, png, jpg, and jpeg

What movie file types will this plugin automatically add Shadowbox to?

swf, flv, f4v, dv, mov, moov, movie, mp4, asf, wm, wmv, avi, mpg and mpeg

What audio file types will this plugin automatically add Shadowbox to?

mp3 and aac

When I click on my YouTube links I see the full YouTube web site and not just my video. What is wrong?

You have probably used the wrong form of the YouTube URL. If you used something like http://www.youtube.com/watch?v=3D3kFn_3xRY that will disaply the YouTube website and not just the video. To just get the video use a link that looks like http://www.youtube.com/v/3D3kFn_3xRY.

How can I use a custom Shadowbox skin without having to worry about it being deleted during the upgrade process?

In version 3.0.0.0 there are now 2 parts to the skin, the markup file and the CSS. Place your custom skin in a location where it will not get removed. For example in your current themes directory. Below is an example:

wp-content/themes/yourthemename/shadowbox-custom-skin 

Once you have placed the skin in this directory you will need to add a few lines to your themes functions.php file. Below is some sample code:

function shadowbox_custom_markup($markup) {
    $markup = 'http://example.org/wp-content/themes/yourthemename/shadowbox-custom-skin/markup.js';
    return $markup;
}
add_filter('shadowbox-markup', 'shadowbox_custom_markup');

function shadowbox_custom_css($css) {
    $css = 'http://example.org/wp-content/themes/yourthemename/shadowbox-custom-skin/shadowbox.css';
    return $css;
}
add_filter('shadowbox-css', 'shadowbox_custom_css');

You do not necessarily have to do both. It is possible to only load a custom markup or only a custom css.

Can I selectively load Shadowbox on pages that need it?

Yes. However this functionality requires WordPress 2.8. If you are running WordPress 2.8 and you would like to enable this functionality visit Settings -> Shadowbox JS and set Enable Smart Loading to true.

Why isn't this plugin working?

Check to make sure that you have <?php wp_head(); ?> in your themes header.php and <?php wp_footer(); ?> in your themes fotoer.php. See the default WordPress theme for examples. Also see the FAQ below.

This plugin has stopped working since I installed another plugin or another plugin has stopped working since I installed this plugin. What can I do?

Try changing the Javascript Library used by this plugin to something other than 'None' on the Shadowbox JS settings page in the WordPress admin.